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"Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms. The algorithms offered include: * MAS5 Statistical algorithm * Probe Logarithmic Intensity Error Estimation (PLIER) * Robust Multichip Analysis (RMA)"

"Affymetrix has recently decided to provide their main GeneChip analysis software at no charge. This is the new "GeneChip Operating Software", GCOS, which folds the old "Micro Array Suite"(MAS) and "Micro DB" into a single program. Previously this program would have sold for something like $6000 a license. Currently it is free to download and can be run on PCs running Windows 2000. (It may also run on Windows XP machines--validation of the program under this Operating System is being done by Affymetrix.) This is a bold move on their part, but I'm convinced that it is a very clever one. Nevertheless, Affy is clearly quaking with fear over this decision and have not really made any great announcement of it that I'm aware of. Thus far to my mind, the killer application provided by GCOS is a scatter plot with fold-difference lines on it. Take any two chips from the same experiment and plot them against each other. You can click on any point and get the name of the gene and the signal strengths, etc. Further you can click and "Info" button and be taken to Affy's NetAffx site to see more information about the gene of interest. Of course, same as will other biological data, if you haven't done replicates you might be looking at random noise. But that caveat aside if you focus on the 10x or 30x fold changes where one of the signals is reasonably high (above 100 at least) you should gather a list of interesting genes that can be followed up. "

"Software Analysis for Affymetrix GeneChip Arrays"